“Digital PCR” refers to a method in which individual nucleic acid molecule present in a sample are distributed to many separate reaction volumes (e.g., chambers or aliquots) prior to PCR amplification of one or more target sequences. The concentration of individual molecules in the sample is adjusted so that after distribution each reaction volume contains fewer than one discrete polynucleotide molecule (or aggregate of linked polynucleotide molecules), and most chambers contain zero or one molecule. Amplification of a target sequence results in a binary digital output in which each chamber is identified as either containing or not containing the PCR product indicative of the presence of the corresponding target sequence. A count of reaction volumes containing detectable levels of PCR end-product is a direct measure of the absolute nucleic acids quantity. In one version of Digital PCR, polynucleotide molecules are distributed by partitioning them into separate reaction volumes. One partition method uses the BioMark™ 12.765 Digital Array (Fluidigm Corp., South San Franscisco, Calif.). This chip utilizes integrated channels and valves that partition mixtures of sample and reagents into 765 nanolitre volume reaction chambers. DNA molecules in each mixture are randomly partitioned into the 765 chambers of each panel. The chip is then thermocycled and imaged on Fluidigm's BioMark real-time PCR system and the positive chambers that originally contained 1 or more molecules can be counted by the digital array analysis software. For discussions of Digital PCR see, for example, Vogelstein and Kinzler, 1999, Proc Natl Acad Sci USA 96:9236-41; McBride et al., U.S. Patent Application Publication No. 20050252773, especially Example 5;
Copy number variations (CNVs) are the gains or losses of genomic regions which range from 500 bases on upwards in size (often between five thousand and five million bases). Whole genome studies have revealed the presence of large numbers of CNV regions in human and a broad range of genetic diversity among the general population. CNVs have been the focus of many recent studies because of their roles in human genetic disorders. See, for example Iafrate et al., 2004, Detection of large-scale variation in the human genome. Nat Genet 36: 949-951; Sebat et al., 2004, Large-scale copy number polymorphism in the human genome. Science 305: 525-528; Redon et al., 2006, Global variation in copy number in the human genome. Nature 444: 444-454; Wong et al., 2007, A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 80: 91-104; Ropers, 2007, New perspectives for the elucidation of genetic disorders. Am J Hum Genet 81: 199-207; Lupski, 2007, Genomic rearrangements and sporadic disease. Nat Genet 39: S43-S47, each of which is incorporated by reference. Aneuploidy, such as trisomy or whole chromosome deletion, is a limiting type of copy number variation associated with a variety of human diseases.